9PI6 | pdb_00009pi6

Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form.Mutations: K166A, E167A, C254S, C455S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1URJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2% PEG 8,000, 100mM Hepes, pH 7.0, 40mM MgCl2, 2mM DTT, 1mM Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.348	α = 90
b = 139.779	β = 111.09
c = 98.869	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979300	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.75	92.42	100	0.107	0.151	0.107	0.979	7.2	2		59491

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.83	100		0.495	0.703	0.497	0.545	1.8	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.75	92.417	59480	2972	99.97	0.181	0.1771	0.1864	0.2609	0.2669	RANDOM	38.589

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.207		0.49	-1.43		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.078
r_dihedral_angle_6_deg	14.728
r_dihedral_angle_2_deg	13.359
r_lrange_it	8.913
r_lrange_other	8.913
r_dihedral_angle_1_deg	6.872
r_scangle_it	5.362
r_scangle_other	5.349
r_mcangle_it	4.601
r_mcangle_other	4.601
r_scbond_it	3.304
r_scbond_other	3.296
r_mcbond_it	2.855
r_mcbond_other	2.853
r_angle_refined_deg	1.693
r_angle_other_deg	0.518
r_nbd_refined	0.222
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.183
r_nbd_other	0.169
r_symmetry_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.022
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16177
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing